The exit status of the task that caused the workflow execution to fail was: 143.
The full error message was:
Error executing process > 'callVariants (4)'
Caused by:
Process `callVariants (4)` terminated with an error exit status (143)
Command executed:
#!/usr/bin/env bash
# Convert the list into a string separated by spaces
bedString="/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c1/a99113ba731f6e2252df62b0b4a015/ZNF880_M07764_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/b7/535426ced0b9ae430a72cc055f21bb/PRGR_PRGR_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/21/0c9370a459559d011e64fc00752c86/GRHL2_M08129_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/99/afbc97441d59ec053d592bba0abec0/STAT1_M08013_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/91/d21046c67804af637d0e71ebebd212/ZNF543_M08347_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/24/ff782513b7f05429d71dc1d2e180df/KLF4_MA0039.4_TOBIAS_TF_binding_sites-sorted.bed 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/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/aa/f38faca5e1d1550161ba39cb6925b9/ZNF460_MA1596.1_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/3d/67cc86d395af86ce1f7a8d99494151/FOSL1_M07833_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/43/53e949ccdc0f335ed278c69886d3b1/SPIB_MA0081.2_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/10/b0c7127fe6a1c366b9fa78709b0869/ZNF552_M07655_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/07/42a3fc14d69a2cbb4b21fddfbe3a20/MAFG_MAFG_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/f8/1e56e23528f18e0c875c643cb977d1/CEBPA_M08076_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/eb/0d305d97b4cc8de027245061bca1dc/ZN317_ZN317_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/9c/d64d5548b8b0d8defe2463be98575b/HXA13_HXA13_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/28/3111b3e0e4c41c2970fec7ab02a8ec/PAX5_M08227_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c9/dc123ddfd1f767d3efeeda867e7f34/POU2F2_M07975_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/9b/0db281eb69fb642382d8324cf90267/ZNF141_M07586_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/41/cd26d77c7888fd341b10243ee07150/KLF10_M08246_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/f2/22f6757da57306ccd8b35ad86a7f5d/PEBB_PEBB_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/b2/a809c705da23fc0b346edc79786561/FOXH1_MA0479.1_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/76/8e8f08dea2f126847b49a3ad6bfdcd/ZNF169_M07645_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/15/d8e2e545fa227739df6ea94c364259/MYCN_MA0104.4_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/71/2df6c75f403440857596674e117e3e/RUNX2_RUNX2_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/3a/9f7531e73ef2fafaa8f43212ab1fad/IRF4_IRF4_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/10/f3b3abc91e199816d4ed58b0afad75/MAFK_M07840_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/31/8efdcfb29621a9fc199f85f7771305/ZNF805_M07753_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/09/0c4ab718f978c19c4f7e572b2ec204/ZNF74_M07675_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/a3/3e59f4ab91f57c44427dbe18860dc2/CTCF_M07922_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/22/d3b543ecbb7f670c0b5ae7d56a4aeb/COE1_COE1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/7d/d20e7a00ea8a03afae85f637e206e2/RORG_RORG_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/31/cde8ee8eb8dd9026b40dc3132fe615/ZNF479_M07673_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/72/e29796c5954040d3fefde96dffa606/STAT1_M08230_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/94/f0c814f65897dfff2b7b2793fa1af2/E2F1_E2F1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/7c/dfb361ec9ccb6d72aeb626b483224c/ZN329_ZN329_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/8f/b38b1690564389a6e24c0c0c72230a/ZNF136_MA1588.1_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/55/07455ae6ee7c9612ccf5696debdb28/MEF2C_MA0497.1_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/65/3b2a080cfe24b830ec8dfa3da909f3/ZNF669_M08367_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/e7/6fdf7b4ca60105604c1f0f806fecf5/ZKSC1_ZKSC1_HUMAN.H11MO.0.B_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/f4/c9159b1c2fbcb062fe91d39578cd5d/HXC9_HXC9_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/32/2eaaa3d2060d981c6fe39070f42d69/ZNF81_M07728_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/d4/3aa3599fce21a375fabd7db6cfa604/ZN341_ZN341_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/ef/fa500843c1aab6ddb839cec2425d46/OZF_OZF_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/79/82009872ff6d0109b1e74253bd2105/ZNF100_M07715_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/a5/b5c6d25b42854843eb4ae4c7e9dba7/ZNF669_MA1985.1_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c9/1389c0bdb32ecd5c7de11850e19d33/ZBTB6_ZBTB6_HUMAN.H11MO.0.C_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/27/30b052abe5419bfc2063255c96ed01/YY1_M08237_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/ef/a500b25ca0ad06c2a1a74662a8725b/MYCN_MYCN_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/ab/a3bbd840b9d5a2aaff0a52fb8335a6/ZNF528_M08249_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/25/b1e61f504c28b69248ad7ad2520b5d/ZNF182_M07597_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/15/c7bf249226b6bd4fccf152e31807ce/ZNF574_M08294_2.00_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/46/6020da44253be9448dd88c2d036dd5/SNAI2_SNAI2_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/ba/4bd0bc36049f7520068af319ee311d/CTCF_M07902_2.00_TOBIAS_TF_binding_sites-sorted.bed"
# Split the string into an array in bash
IFS=' ' read -r -a bedArray <<< "${bedString}"
# Count number of elements in array
echo "No. of BED files: " "${#bedArray[@]}"
echo "First BED: " "${bedArray[0]}"
mpileup_module() {
local BEDFILES="$1"
local BAMLIST="$2"
local DATAID="$3"
local FASTAFILE="$4"
bash /mnt/runParallelMpileup.sh "$BEDFILES" "$BAMLIST" "$DATAID" "$FASTAFILE"
}
# export function to be used in parallel
export -f mpileup_module
# determine the number of available CPU cores
num_cores=$(nproc)
echo "Number of cores: "$num_cores
# set arguments
bedFileArray="${bedArray[@]}"
bamPathList="36GFMD3.bamlist.txt"
dataID="36GFMD3"
# Use GNU Parallel to run the commands in parallel using all available cores
parallel -j "$num_cores" mpileup_module ::: "${bedArray[@]}" ::: "${bamPathList}" ::: "${dataID}" ::: "/refs/GRCh38_no_alt_GCA_000001405.15.fasta"
Command exit status:
143
Command output:
No. of BED files: 136
First BED: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c1/a99113ba731f6e2252df62b0b4a015/ZNF880_M07764_2.00_TOBIAS_TF_binding_sites-sorted.bed
Number of cores: 128
Command wrapper:
No. of BED files: 136
First BED: /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/c1/a99113ba731f6e2252df62b0b4a015/ZNF880_M07764_2.00_TOBIAS_TF_binding_sites-sorted.bed
Number of cores: 128
=>> PBS: job killed: walltime 86518 exceeded limit 86400
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Resource Usage on 2024-03-15 18:37:50.269188:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
JobId: 6395841.pbs101
Project: 12003580
Exit Status: -29
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NCPUs: Requested(64), Used(64)
CPU Time Used: 249:45:25
Memory: Requested(100gb), Used(104857964kb)
Vmem Used: 8749569504kb
Walltime: Requested(24:00:00), Used(24:02:09)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Execution Nodes Used: (x1001c2s1b0n0:ncpus=64:mem=104857600kb)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
No GPU-related information available for this job.
Work dir:
/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/f4/7f279222f36b54ec4dbdfe26d569e7
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
nextflow -log nextflow-logs/.nextflow.log run -resume main.nf --run_mode subset --dataset_id_list cluster-input-dir/manifests/dataset-manifest-rerun-long.txt -c nextflow_cluster.config -with-dag workflow-reports/longjobs/v2/dag-20240314-18.30.html -with-report workflow-reports/longjobs/v2/report-20240314-18.30.html -with-timeline workflow-reports/longjobs/v2/timeline-20240314-18.30.html639dfd5d1ccea4e908c827f952f68e8e4e6c7739-63ed-44aa-ad25-a94feece01e0These plots give an overview of the distribution of resource usage for each process.
This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.